Starting phenix.real_space_refine on Fri Jul 3 01:03:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vz4_32220/07_2026/7vz4_32220.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vz4_32220/07_2026/7vz4_32220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vz4_32220/07_2026/7vz4_32220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vz4_32220/07_2026/7vz4_32220.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vz4_32220/07_2026/7vz4_32220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vz4_32220/07_2026/7vz4_32220.map" } resolution = 1.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 14 5.16 5 C 6538 2.51 5 N 2223 2.21 5 O 2780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11843 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "C" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 826 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 2970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2970 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2969 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 2.21, per 1000 atoms: 0.19 Number of scatterers: 11843 At special positions: 0 Unit cell: (120.25, 73.45, 114.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 288 15.00 O 2780 8.00 N 2223 7.00 C 6538 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 153.7 milliseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1384 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 73.7% alpha, 3.2% beta 145 base pairs and 274 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.094A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.370A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.093A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.370A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 123 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.837A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.088A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.485A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.837A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.088A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 412 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 372 hydrogen bonds 744 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 274 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1773 1.33 - 1.45: 4672 1.45 - 1.57: 5599 1.57 - 1.69: 576 1.69 - 1.81: 24 Bond restraints: 12644 Sorted by residual: bond pdb=" N MET A 120 " pdb=" CA MET A 120 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.67e+01 bond pdb=" N MET E 120 " pdb=" CA MET E 120 " ideal model delta sigma weight residual 1.453 1.487 -0.034 8.30e-03 1.45e+04 1.65e+01 bond pdb=" O3' DA J -1 " pdb=" P DT J 0 " ideal model delta sigma weight residual 1.607 1.664 -0.057 1.50e-02 4.44e+03 1.45e+01 bond pdb=" O3' DT I 1 " pdb=" P DC I 2 " ideal model delta sigma weight residual 1.607 1.663 -0.056 1.50e-02 4.44e+03 1.41e+01 bond pdb=" C ARG E 42 " pdb=" N PRO E 43 " ideal model delta sigma weight residual 1.330 1.373 -0.043 1.19e-02 7.06e+03 1.31e+01 ... (remaining 12639 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 14834 1.39 - 2.78: 3007 2.78 - 4.17: 442 4.17 - 5.57: 28 5.57 - 6.96: 8 Bond angle restraints: 18319 Sorted by residual: angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 112.90 106.65 6.25 9.60e-01 1.09e+00 4.23e+01 angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 112.90 106.69 6.21 9.60e-01 1.09e+00 4.19e+01 angle pdb=" N GLN G 24 " pdb=" CA GLN G 24 " pdb=" C GLN G 24 " ideal model delta sigma weight residual 113.23 107.67 5.56 1.24e+00 6.50e-01 2.01e+01 angle pdb=" N GLN C 24 " pdb=" CA GLN C 24 " pdb=" C GLN C 24 " ideal model delta sigma weight residual 113.23 107.69 5.54 1.24e+00 6.50e-01 2.00e+01 angle pdb=" N LYS F 79 " pdb=" CA LYS F 79 " pdb=" C LYS F 79 " ideal model delta sigma weight residual 113.30 107.82 5.48 1.34e+00 5.57e-01 1.67e+01 ... (remaining 18314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 4106 16.80 - 33.61: 1082 33.61 - 50.41: 1168 50.41 - 67.21: 464 67.21 - 84.02: 20 Dihedral angle restraints: 6840 sinusoidal: 4688 harmonic: 2152 Sorted by residual: dihedral pdb=" CG ARG A 131 " pdb=" CD ARG A 131 " pdb=" NE ARG A 131 " pdb=" CZ ARG A 131 " ideal model delta sinusoidal sigma weight residual -90.00 -134.77 44.77 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG E 131 " pdb=" CD ARG E 131 " pdb=" NE ARG E 131 " pdb=" CZ ARG E 131 " ideal model delta sinusoidal sigma weight residual -90.00 -134.76 44.76 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA ASP C 90 " pdb=" CB ASP C 90 " pdb=" CG ASP C 90 " pdb=" OD1 ASP C 90 " ideal model delta sinusoidal sigma weight residual -30.00 -85.59 55.59 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 6837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1104 0.052 - 0.105: 629 0.105 - 0.157: 255 0.157 - 0.210: 74 0.210 - 0.262: 20 Chirality restraints: 2082 Sorted by residual: chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA LEU F 97 " pdb=" N LEU F 97 " pdb=" C LEU F 97 " pdb=" CB LEU F 97 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2079 not shown) Planarity restraints: 1316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA J 47 " -0.022 2.00e-02 2.50e+03 1.01e-02 2.83e+00 pdb=" N9 DA J 47 " 0.019 2.00e-02 2.50e+03 pdb=" C8 DA J 47 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DA J 47 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DA J 47 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DA J 47 " -0.011 2.00e-02 2.50e+03 pdb=" N6 DA J 47 " 0.000 2.00e-02 2.50e+03 pdb=" N1 DA J 47 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DA J 47 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DA J 47 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA J 47 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 47 " -0.022 2.00e-02 2.50e+03 9.98e-03 2.74e+00 pdb=" N9 DA I 47 " 0.019 2.00e-02 2.50e+03 pdb=" C8 DA I 47 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DA I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 47 " -0.010 2.00e-02 2.50e+03 pdb=" N6 DA I 47 " -0.001 2.00e-02 2.50e+03 pdb=" N1 DA I 47 " -0.004 2.00e-02 2.50e+03 pdb=" C2 DA I 47 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DA I 47 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA I 47 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -54 " 0.022 2.00e-02 2.50e+03 9.72e-03 2.60e+00 pdb=" N9 DA I -54 " -0.020 2.00e-02 2.50e+03 pdb=" C8 DA I -54 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DA I -54 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I -54 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA I -54 " 0.008 2.00e-02 2.50e+03 pdb=" N6 DA I -54 " 0.002 2.00e-02 2.50e+03 pdb=" N1 DA I -54 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DA I -54 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA I -54 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DA I -54 " -0.003 2.00e-02 2.50e+03 ... (remaining 1313 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 754 2.71 - 3.26: 9628 3.26 - 3.81: 22742 3.81 - 4.35: 31188 4.35 - 4.90: 41308 Nonbonded interactions: 105620 Sorted by model distance: nonbonded pdb=" NH1 ARG G 11 " pdb=" O2 DT J -42 " model vdw 2.167 3.120 nonbonded pdb=" NH1 ARG C 11 " pdb=" O2 DT I -42 " model vdw 2.169 3.120 nonbonded pdb=" CB SER E 57 " pdb=" OE1 GLU E 59 " model vdw 2.469 3.440 nonbonded pdb=" CB SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.469 3.440 nonbonded pdb=" O5' DG I -58 " pdb=" O4' DG I -58 " model vdw 2.503 2.432 ... (remaining 105615 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid -72 through -1 or resid 1 through 72)) selection = (chain 'J' and (resid -72 through -1 or resid 1 through 72)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.040 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.057 12644 Z= 0.698 Angle : 1.117 6.958 18319 Z= 0.888 Chirality : 0.077 0.262 2082 Planarity : 0.003 0.013 1316 Dihedral : 28.811 84.018 5456 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.97 % Allowed : 9.71 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.27), residues: 730 helix: 0.29 (0.19), residues: 532 sheet: None (None), residues: 0 loop : -0.17 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 92 TYR 0.013 0.002 TYR G 57 PHE 0.012 0.002 PHE E 67 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00943 / 0.70 (12644) covalent geometry : angle 1.11691 / 0.89 (18319) hydrogen bonds : bond 0.13905 / 9.63 ( 784) hydrogen bonds : angle 7.52277 / 5.47 ( 1956) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 173 time to evaluate : 0.276 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 177 average time/residue: 0.9188 time to fit residues: 169.7648 Evaluate side-chains 130 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN E 68 GLN F 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.181179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.148346 restraints weight = 7523.851| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 0.34 r_work: 0.3331 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12644 Z= 0.155 Angle : 0.720 7.238 18319 Z= 0.408 Chirality : 0.050 0.242 2082 Planarity : 0.004 0.037 1316 Dihedral : 31.451 81.283 3992 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 0.16 % Allowed : 10.52 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.74 (0.29), residues: 730 helix: 2.48 (0.21), residues: 534 sheet: None (None), residues: 0 loop : -0.06 (0.38), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 35 TYR 0.012 0.002 TYR F 51 PHE 0.012 0.002 PHE A 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.16 (12644) covalent geometry : angle 0.71955 / 0.41 (18319) hydrogen bonds : bond 0.05820 / 4.01 ( 784) hydrogen bonds : angle 3.21313 / 2.42 ( 1956) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.267 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 137 average time/residue: 0.9600 time to fit residues: 137.2240 Evaluate side-chains 133 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 85 optimal weight: 20.0000 chunk 28 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.175361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.140061 restraints weight = 7413.783| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 0.49 r_work: 0.3223 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12644 Z= 0.226 Angle : 0.850 9.646 18319 Z= 0.471 Chirality : 0.056 0.251 2082 Planarity : 0.006 0.048 1316 Dihedral : 31.368 80.481 3992 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.13 % Allowed : 7.77 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.29), residues: 730 helix: 2.35 (0.21), residues: 540 sheet: None (None), residues: 0 loop : 0.01 (0.38), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 42 TYR 0.019 0.003 TYR C 57 PHE 0.013 0.003 PHE E 84 HIS 0.012 0.003 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.23 (12644) covalent geometry : angle 0.85009 / 0.47 (18319) hydrogen bonds : bond 0.07194 / 4.95 ( 784) hydrogen bonds : angle 3.49092 / 2.61 ( 1956) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 130 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 132 average time/residue: 0.9618 time to fit residues: 132.2629 Evaluate side-chains 131 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 93 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.176889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.143105 restraints weight = 7479.563| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 0.39 r_work: 0.3247 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12644 Z= 0.171 Angle : 0.751 8.333 18319 Z= 0.426 Chirality : 0.051 0.238 2082 Planarity : 0.005 0.035 1316 Dihedral : 31.380 81.025 3992 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.97 % Allowed : 7.28 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.76 (0.29), residues: 730 helix: 2.51 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -0.14 (0.37), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 67 TYR 0.015 0.002 TYR C 57 PHE 0.014 0.002 PHE A 67 HIS 0.008 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.17 (12644) covalent geometry : angle 0.75145 / 0.43 (18319) hydrogen bonds : bond 0.06198 / 4.27 ( 784) hydrogen bonds : angle 3.28518 / 2.47 ( 1956) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 130 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 132 average time/residue: 1.0014 time to fit residues: 137.6028 Evaluate side-chains 131 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 68 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 81 optimal weight: 20.0000 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 2 optimal weight: 0.0470 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.177148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.142285 restraints weight = 7512.578| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 0.42 r_work: 0.3233 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12644 Z= 0.171 Angle : 0.742 8.355 18319 Z= 0.422 Chirality : 0.050 0.232 2082 Planarity : 0.005 0.035 1316 Dihedral : 31.332 81.740 3992 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.97 % Allowed : 7.44 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.29), residues: 730 helix: 2.57 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -0.09 (0.37), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 35 TYR 0.016 0.002 TYR C 57 PHE 0.013 0.002 PHE A 67 HIS 0.008 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.17 (12644) covalent geometry : angle 0.74185 / 0.42 (18319) hydrogen bonds : bond 0.06074 / 4.18 ( 784) hydrogen bonds : angle 3.27765 / 2.46 ( 1956) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 129 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 131 average time/residue: 1.0905 time to fit residues: 148.8974 Evaluate side-chains 130 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 24 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 88 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 47 GLN E 68 GLN H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.176361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.142521 restraints weight = 7436.848| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 0.40 r_work: 0.3241 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12644 Z= 0.182 Angle : 0.750 8.550 18319 Z= 0.425 Chirality : 0.050 0.246 2082 Planarity : 0.005 0.039 1316 Dihedral : 31.197 80.029 3992 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.97 % Allowed : 7.44 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.29), residues: 730 helix: 2.52 (0.21), residues: 540 sheet: None (None), residues: 0 loop : 0.04 (0.37), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 67 TYR 0.016 0.002 TYR C 57 PHE 0.012 0.002 PHE A 67 HIS 0.008 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.18 (12644) covalent geometry : angle 0.75035 / 0.43 (18319) hydrogen bonds : bond 0.06342 / 4.37 ( 784) hydrogen bonds : angle 3.32732 / 2.49 ( 1956) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 133 average time/residue: 1.0889 time to fit residues: 150.8056 Evaluate side-chains 133 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 65 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 79 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN D 47 GLN E 68 GLN H 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.176155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.141267 restraints weight = 7416.529| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 0.40 r_work: 0.3238 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12644 Z= 0.187 Angle : 0.765 8.652 18319 Z= 0.431 Chirality : 0.050 0.244 2082 Planarity : 0.005 0.035 1316 Dihedral : 31.170 80.575 3992 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.97 % Allowed : 8.09 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.29), residues: 730 helix: 2.51 (0.21), residues: 540 sheet: None (None), residues: 0 loop : 0.02 (0.37), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 67 TYR 0.016 0.002 TYR C 57 PHE 0.012 0.003 PHE A 67 HIS 0.008 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.19 (12644) covalent geometry : angle 0.76471 / 0.43 (18319) hydrogen bonds : bond 0.06387 / 4.39 ( 784) hydrogen bonds : angle 3.33608 / 2.50 ( 1956) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 133 average time/residue: 1.1357 time to fit residues: 157.3873 Evaluate side-chains 133 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 66 optimal weight: 0.0570 chunk 90 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 43 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 overall best weight: 3.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN D 47 GLN E 68 GLN E 76 GLN H 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.174479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.140513 restraints weight = 7356.164| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 0.45 r_work: 0.3220 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 12644 Z= 0.249 Angle : 0.884 9.540 18319 Z= 0.487 Chirality : 0.057 0.290 2082 Planarity : 0.007 0.046 1316 Dihedral : 31.173 81.509 3992 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.13 % Allowed : 7.44 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.56 (0.29), residues: 730 helix: 2.32 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.12 (0.36), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 35 TYR 0.019 0.003 TYR C 57 PHE 0.013 0.004 PHE E 84 HIS 0.009 0.003 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.25 (12644) covalent geometry : angle 0.88390 / 0.49 (18319) hydrogen bonds : bond 0.07473 / 5.14 ( 784) hydrogen bonds : angle 3.53784 / 2.65 ( 1956) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 127 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 129 average time/residue: 1.1684 time to fit residues: 156.9573 Evaluate side-chains 130 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 11 optimal weight: 0.5980 chunk 84 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN D 47 GLN E 68 GLN E 76 GLN H 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.176426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.141442 restraints weight = 7402.245| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 0.38 r_work: 0.3245 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12644 Z= 0.172 Angle : 0.756 8.035 18319 Z= 0.429 Chirality : 0.051 0.236 2082 Planarity : 0.005 0.036 1316 Dihedral : 31.217 81.311 3992 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.97 % Allowed : 7.77 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.29), residues: 730 helix: 2.47 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.04 (0.37), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 42 TYR 0.014 0.002 TYR D 40 PHE 0.014 0.002 PHE A 67 HIS 0.006 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.17 (12644) covalent geometry : angle 0.75603 / 0.43 (18319) hydrogen bonds : bond 0.06227 / 4.30 ( 784) hydrogen bonds : angle 3.29949 / 2.47 ( 1956) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 130 average time/residue: 1.2059 time to fit residues: 163.3662 Evaluate side-chains 131 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN D 47 GLN E 76 GLN H 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.175724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.141820 restraints weight = 7393.019| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 0.39 r_work: 0.3239 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12644 Z= 0.196 Angle : 0.788 8.689 18319 Z= 0.443 Chirality : 0.052 0.245 2082 Planarity : 0.005 0.037 1316 Dihedral : 31.150 81.725 3992 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.97 % Allowed : 7.77 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.78 (0.29), residues: 730 helix: 2.48 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.04 (0.37), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 42 TYR 0.017 0.002 TYR C 57 PHE 0.012 0.003 PHE A 67 HIS 0.008 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.20 (12644) covalent geometry : angle 0.78751 / 0.44 (18319) hydrogen bonds : bond 0.06582 / 4.52 ( 784) hydrogen bonds : angle 3.37426 / 2.52 ( 1956) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 126 average time/residue: 1.1422 time to fit residues: 149.8558 Evaluate side-chains 130 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 15 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 44 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 1 optimal weight: 0.6980 chunk 82 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN D 47 GLN E 76 GLN H 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.176390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.142664 restraints weight = 7469.746| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 0.38 r_work: 0.3244 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12644 Z= 0.168 Angle : 0.757 8.434 18319 Z= 0.430 Chirality : 0.050 0.236 2082 Planarity : 0.005 0.056 1316 Dihedral : 31.171 81.676 3992 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 0.97 % Allowed : 8.09 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.29), residues: 730 helix: 2.50 (0.21), residues: 540 sheet: None (None), residues: 0 loop : -0.03 (0.37), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG E 42 TYR 0.014 0.002 TYR C 57 PHE 0.014 0.002 PHE E 67 HIS 0.008 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.17 (12644) covalent geometry : angle 0.75726 / 0.43 (18319) hydrogen bonds : bond 0.06245 / 4.30 ( 784) hydrogen bonds : angle 3.30758 / 2.47 ( 1956) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5932.67 seconds wall clock time: 101 minutes 11.12 seconds (6071.12 seconds total)